This paper examines the complex relationship between male circumcision and HIV prevalence and incidence in sub-Saharan African countries that have generalised epidemics. In South Africa, the mean yearly HIV incidence and an estimate of the net reproduction rate of the epidemic (R 0) (in this case, the ratio of the number of HIV-infected persons between 1994 and 2004 to the number of persons infected in 1994 from which they were presumed to have become infected) were computed from antenatal clinic data for the period 1994–2004, and then compared, by province, to prevailing levels of male circumcision (high, medium and low). In South Africa, mean yearly HIV incidence and net reproduction rate of the epidemic were not lower in provinces with higher levels of male circumcision. For thirteen other countries where Demographic and Health Survey data were available, male HIV prevalence in circumcised and non-circumcised groups was compared. A meta-analysis of that data, contrasting male HIV seroprevalence according to circumcision status, showed no difference between the two groups (combined risk ratio [RR] = 0.99, 95% CI = 0.94–1.05). Individual case study analysis of eight of those countries showed no significant difference in seroprevalence in circumcised and uncircumcised groups, while two countries (Kenya and Uganda) showed lower HIV prevalence among circumcised groups, and three countries (Cameroon, Lesotho and Malawi) showed higher HIV prevalence among circumcised groups. In most countries with a complex ethnic fabric, the relationship between men's circumcision status and HIV seroprevalence was not straightforward, with the exception of the Luo in Kenya and a few groups in Uganda. These observations put into question the potential long-term effect of voluntary circumcision programmes in countries with generalised HIV epidemics.